Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Smoothness may be a problem. If you choose different weights for the regularization term, you may end up with different thickness values. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Jürgen Hänggi [j.haenggi@psychologie.uzh.ch] Sent: Friday, June 14, 2013 3:44 AM To: Freesurfer Mailinglist Subject: [Freesurfer] Reviewer not satisfied
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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true, although this is less of a problem for us as our main regularization is to assume that the surfaces are well-fit by quadratic patches, not planes, so more smoothness doesn't necessarily cause the surface to retract as in other more typical regularizations
On Fri, 14 Jun 2013, Chen, Yasheng wrote:
Smoothness may be a problem. If you choose different weights for the regularization term, you may end up with different thickness values. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Jürgen Hänggi [j.haenggi@psychologie.uzh.ch] Sent: Friday, June 14, 2013 3:44 AM To: Freesurfer Mailinglist Subject: [Freesurfer] Reviewer not satisfied
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Chen
Thanks a lot for your info
Cheers Jürgen
On [DATE], "Chen, Yasheng" <[ADDRESS]> wrote:
Smoothness may be a problem. If you choose different weights for the regularization term, you may end up with different thickness values. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Jürgen Hänggi [j.haenggi@psychologie.uzh.ch] Sent: Friday, June 14, 2013 3:44 AM To: Freesurfer Mailinglist Subject: [Freesurfer] Reviewer not satisfied
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files?
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
.H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want.
Bruce
On Tue, 18 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files?
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
Dear Bruce
Yes, the .max and the .min files were produced, but how to access the values in it. Is there a possibility to import these files into MATLAB?
Thanks in advance Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
.H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want.
Bruce
On Tue, 18 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files?
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
--------------------------------------------------------------------------->>>> -
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------
read_curv.m should do the trick On Wed, 19 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Yes, the .max and the .min files were produced, but how to access the values in it. Is there a possibility to import these files into MATLAB?
Thanks in advance Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
.H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want.
Bruce
On Tue, 18 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files?
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Dear Bruce
Thanks a lot for the hint
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
read_curv.m should do the trick On Wed, 19 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Yes, the .max and the .min files were produced, but how to access the values in it. Is there a possibility to import these files into MATLAB?
Thanks in advance Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
.H is mean and .K is Gaussian curvature. It should also write a .max and .min, doesn't it? Those are the principal curvatures that you want.
Bruce
On Tue, 18 Jun 2013, Jürgen Hänggi wrote:
Dear Bruce
Thanks a lot for the info. It worked fine, but how can I open the resulting .H and .K files?
Cheers Jürgen
On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:
Hi Jürgen
you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution.
cheers Bruce
p.s. I think you want -w -max and -w -min flags for it
On Fri, 14 Jun 2013, Jürgen Hänggi wrote:
Dear FS experts
In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition.
We wrote the following:
The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter.
Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters".
Is this 1-3 mm or rather 3-5 mm or any other value?
Thanks in advance for any suggestion Regards Jürgen Hänggi
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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